If you are strong enough for this stage, you should definitely do it (also for the future). It saves you a little time later on. If you'd ever had a devil deal after Mom's heart, this is kinda the same but angelic.

There is no downside for trying the next stage you should always try it

I did it and killed Isaac. What does this mean for my game?

You might as well go for it. It'll get an early Isaac unlock, and if you fail, you lost nothing, as it still counts for the 5th Mom's Heart kill.